Hi Daniel,
Theoretically speaking, Transfer Functions are defined when all initial conditions on a system are set to zero.
However, if initial conditions need to be changed, it has to be realized in state space (by using integrator in continuous time and unit delays in discrete time).
To specify initial conditions, convert your system to state-space model using the "tf2ss" command and use the State-space block in Simulink.
For more information on this, refer to the following documentation link:
Best,
Farouk